targeting of parallel c-myc g-quadruplex by dimeric ... · tc-p7 587 590 a 611 625 24 35 0.13a 0.13...
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Supporting information for:
Targeting of parallel c-myc G-quadruplex by dimeric
cyanine dye supramolecular assembly: dependence on
the linker length
Lijia Yu, a,b
Qianfan Yang, *a Junfeng Xiang,
*
a Hongxia Sun,
a Lixia Wang,
a Qian Li,
a Aijiao Guan,
a and Yalin Tang*
a
a Beijing National Laboratory for Molecular Sciences, Centre for
Molecular Science, State Key Laboratory for Structural Chemistry for
Unstable and Stable Species, Institute of Chemistry, Chinese Academy of
Sciences (ICCAS), Beijing, 100190, P.R. China.
b University of Chinese Academy of Sciences, Beijing, China
Email: tangyl@iccas.ac.cn, jfxiang@iccas.ac.cn and
yangqf@iccas.ac.cn; Tel: 86 10 62558322 or 86 1 0 82617304.
Electronic Supplementary Material (ESI) for Analyst.This journal is © The Royal Society of Chemistry 2015
S-2
1. The spectra characteristics of TC and TC-P3-7.
Table S1. Absorption and emission maxima (λmax), Stokes’s shifts (∆νst) and quantum yields (Φ) of dyes TC
and TC-P3-7.
Complex λmax(Abs) (nm) λmax(Em)
(nm)
Stoke shift
∆νst (nm)
Φ
TC 586 607 21 0.17a
TC-P3 586 609 23 0.21 a
TC-P4 587 610 23 0.11 a
TC-P5 586 611 23 0.21 a
TC-P6
TC-P7
587
590
611
625
24
35
0.13 a
0.13 a
a The fluorescence quantum yield (Φ) were measured in DMSO solution using crystal violet in methanol as the reference.
2. Absorption and fluorescence spectra of TC-P4
400 500 600 700 8000.0
0.2
0.4
0.6
Abs
orba
nce
Wavlength(nm)
H-aggregate
Dimer
monomer
600 650 700 7500
40
80
120
160
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
H-aggregate
Dimer
monomer
604 nm
597.8nm
587 nm
Figure S1. The absorbance (left) and fluorescence emission (right) of TC-P4 in MeOH (red), CH2Cl2
(blue) and water (black).
As shown in Figure S1, TC-P4 shows different assembly in different solvents. TC-P4
shows strong enhancement fluorescence intensity around 604 nm assigned to monomer in
CH2Cl2, moderate enhancement fluorescence intensity around 597.8 nm assigned to dimer in
MeOH, and strongly quenched around 587 nm assigned to H-aggregates in PBS. It is well
documented that the fluorescence of H-aggregates is strong quenched in aqueous solution1.
3. The stability of TC-P3-7
S-3
20 30 40 50 60 70 80 90 100Temperature(oC)
TC-P3
TC-P4
TC-P5
TC-P6
TC-P7
Figure S2. The stability of dyes TC-P3-7 was carried out in PBS. The absorbance spectra of these dyes were
normalized at 470 nm.
4. The sequence and origin of 4 oligonucleotides in the study
Table S2. Sequence and origin of 4 oligomers
Sequence (from 5 to 3) Motifs Origin
c-myc 22 TGAGGGTGGGTAGGGTGGGTAA Parallel G-quadruplex Oncogenic promoter
c-myc TGAGGGTGGGGAGGGTGGGGAA Parallel G-quadruplex Oncogenic promoter
CT Linear double-stranded Calf thymus
S17 CCAGTTCGTAGTAACCC Single-Stranded
5. The Structure identification of 4 sequences by CD spectroscopy.
240 260 280 300 320-20
-10
0
10
20
30
40
CD
(mdg
ree)
Wavelength(nm)
c-myc c-myc22 CT S17
Figure S3. The CD spectra for 4 oligomers in 10 mM PBS (K+).
6. UV titration spectra of c-myc with TC-P3, TC-P5, TC-P6 and TC-P7.
400 500 600 700 8000.0
0.2
0.4
0.6
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P3]=5 M
[c-myc]:[TC-P3] 0
0.25
0.5
0.75
1
2
4
6
8
400 500 600 700 8000.0
0.1
0.2
0.3
0.4
0.5
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P3]=5 M
[CT]:[TC-P3]
0
1
2
4
8
400 500 600 700 800
0.0
0.1
0.2
0.3
0.4
0.5
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P3]=5 M
[S17]:[TC-P3]
0
1
2
4
8
S-4
400 500 600 700 8000.0
0.1
0.2
0.3
0.4
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P5]=5 M
[c-myc]:[TC-P5]
0
0.25
0.5
0.75
1
2
4
6
8
400 500 600 700 8000.00
0.04
0.08
0.12
0.16
0.20
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P5]=5 M
[CT]:[TC-P5] 0
1
2
4
8
400 500 600 700 8000.00
0.05
0.10
0.15
0.20[TC-P5]=5 M
[S17]:[TC-P5]
0
1
2
4
8
Abs
orba
nce
(AU
)
Wavelength (nm)
400 500 600 700 8000.0
0.1
0.2
0.3
0.4
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P6]=5 M
[c-myc]:[TC-P6]
0
0.25
0.5
0.75
1
2
4
6
8
400 500 600 700 8000.0
0.1
0.2
0.3[TC-P6]=5 M
[CT]:[TC-P6]
0
1
2
4
8A
bsor
banc
e (A
U)
Wavelength (nm)400 500 600 700 800
0.00
0.05
0.10
0.15
0.20
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P6]=5 M
[S17]:[TC-P6]
0
1
2
4
8
400 500 600 700 8000.00
0.05
0.10
0.15
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P7]=5
[c-myc]:[TC-P7]
0
0.25
0.5
0.75
1
2
4
6
8
400 500 600 700 800
0.00
0.05
0.10
Abs
orba
nce
(AU
)
Wavelength (nm)
[TC-P7]=5 M
[CT]:[TC-P7]
0
1
2
4
8
400 500 600 700 800
0.00
0.04
0.08
Ab
so
rba
nce
(A
U)
Wavelength (nm)
[TC-P7]=5
[S17]:[TC-P7]
0
1
2
4
8
Figure S4. The UV titration spectra of 5 μM TC-P3 and TC-P5-7 in 10 mM PBS with parallel G-quadruplex
c-myc, duplex CT and single-stranded S17.
7. The FL titration spectra of c-myc with TC-P3, TC-P5, TC-P6 and TC-P7.
600 650 700 7500
30
60
90
Fluo
resc
ence
Inte
nsity
Wavelenth(nm)
[TC-P3]=5 M
[c-myc]:[TC-P3]
0
0.25
0.5
0.75
1
2
4
6
8
600 650 700 7500
4
8
12 [TC-P3]=5 M
[CT]:[TC-P3]
0
1
2
4
8
Fluo
resc
ence
Inte
nsity
Wavelength(nm)600 650 700 750
0
2
4
6
8
10
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
[TC-P3]=5 M
[S17]:[TC-P3]
0
1
2
4
8
600 650 700 7500
40
80
120
160
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
[TC-P5]=5
[c-myc]:[TC-P5]
0
0.25
0.5
0.75
1
2
4
6
8
600 650 700 7500
5
10
15
20
25 [TC-P5]=5 M
[CT]:[TC-P5] 0
1
2
4
8
Fluo
resc
ence
Inte
nsity
Wavelength(nm)600 650 700 750
0
3
6
9
12
15
18
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
[TC-P5]=5 M
[S17]:[TC-P5]
0
1
2
4
8
S-5
600 650 700 7500
40
80
120Fl
uore
scen
ce In
tens
ity
Wavelength(nm)
[TC-P6]=5 M
[c-myc]:[TC-P6]
0
0.25
0.5
0.75
1
2
4
6
8
600 650 700 7500
5
10
15
20
25
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
[TC-P6]=5 M
[CT]:[TC-P6]
0
1
2
4
8
600 650 700 7500
3
6
9
12
15
[TC-P6]=5 M
[S17]:[TC-P6]
0
1
2
4
8
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
600 650 700 7500
30
60
90
120
150
Flu
ore
scen
ce In
ten
sity
Wavelength(nm)
[TC-P7]=5
[c-myc]:[TC-P7]
0
0.25
0.5
0.75
1
2
4
6
8
600 650 700 7500
4
8
12
16
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
[TC-P7]=5
[CT]:[TC-P7]
0
1
2
4
8
600 650 700 7500
2
4
6
Fluo
resc
ence
Inte
nsity
Wavelength(nm)
[TC-P7]=5 M
[S17]:[TC-P7]
0
1
2
4
8
Figure S5. The FL titration spectra of 5 μM TC-P3 and TC-P5-7 in 10 mM PBS with parallel G-quadruplex
c-myc, duplex CT and single-stranded S17.
0.0 0.2 0.4 0.6 0.8 1.00
10
20
30
40
50
(F/(F
0-1)
)*([T
C-P
3]/([
TC-P
3]+[
c-m
yc]))
[TC-P3]/([TC-P3]+[c-myc])0.0 0.2 0.4 0.6 0.8 1.0
0
4
8
12
16
(F/(F
0-1)
)*([T
C-P
4]/([
TC-P
4]+[
c-m
yc]))
[TC-P4]/([TC-P4]+[c-myc])
0.0 0.2 0.4 0.6 0.8 1.00
2
4
6
8
10
12
(F/(F
0-1)
)*([T
C-P
5]/([
TC-P
5]+[
c-m
yc]))
[TC-P5]/([TC-P5]+[c-myc])0.0 0.2 0.4 0.6 0.8 1.0
0
4
8
12
(F/(F
0-1)
)*([T
C-P
6]/([
TC-P
6]+[
c-m
yc]))
[TC-P6]/([TC-P6]+[c-myc])
0.0 0.2 0.4 0.6 0.8 1.00
4
8
12
16
F/(F
0-1)
)*([T
C-P
7]/([
TC-P
7]+[
c-m
yc]))
[TC-P7]/([TC-P7]+[c-myc]) Figure S6. Job plot analysis2. TC-P3 and TC-P5-7 were mixed with c-myc at different ratio in 10 mM PBS.
S-6
8.Inhibition activity of TC-P3 and TC-P5-7 on the peroxidase activity of G4/hemin
complexes.
Figure S7. Inhibition of activity of TC-P3 (a) and TC-P5-6 (b-d) on the peroxidase activity of G4/Hemin
complexes. The curves represent the changes of the product concentration (absorbance at 415 nm) of peroxidase
reaction with 2 min. The G4/hemin peroxidase reaction in the absence of dyes was used as a control.
9. Molecular docking experiment
S-7
Figure S8. Molecular models showing interaction of TC-P3-7 (a-f) with G-quadruplex (PDB: 2L7V).
TC-P3-7 could stack on both ends of G-quadruplex.
10. The flow cytometric analysis. Table S3. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P3
Cell Cell No. TC-P3 Uptake( /105 cell)
control stained control stained Δ/ uptake
No.
CRL2614 30059 100000 585 79716 79131
Hela 100000 100000 99 11475 11376
Table S4. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P4
Cell Cell No. TC-P4 Uptake( /105 cell)
control stained control stained Δ/ uptake
S-8
No.
CRL2614 100000 100000 102 51601 51499
Hela 100000 100000 265 91235 90970
Table S5. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P5
Cell Cell No. TC-P5 Uptake( /105 cell)
control stained control stained Δ/ uptake
No.
CRL2614 100000 100000 109 3665 3556
Hela 100000 100000 94 51012 50918
Table S6. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P6
Cell Cell No. TC-P6 Uptake( /105 cell)
control stained control stained Δ/ uptake No.
CRL2614 100000 100000 109 867 758
Hela 100000 100000 94 47654 47560
Table S7. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P7
Cell Cell No. TC-P7 Uptake( /105 cell)
control stained control stained Δ/ uptake No.
CRL2614 100000 100000 109 2103 1994
Hela 100000 100000 94 13341 13247
Reference
1. U. Rösch, S. Yao, R. Wortmann and F. Würthner, Angewandte Chemie, 2006, 118, 7184-7188.
2. P. Job, Annali di Chimica Applicata, 1928, 9, 113-203.
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